that's intended behaviour. The image comes with a 50MB FAT partition (that's what you see) and a 2nd ext4 partition. In order to copy there you'd have to scp over directly to the 2nd partition. For instance using "WinSCP" if you're on Windows. In order to resize the 2nd partition to the full rest of the 16GB card I'm not sure how to do on Windows. You may however use a Linux system (e.g. Live system - see e.g galileo-debian / Wiki / How to expand the root filesystem to use the entire SD card) to do so. e.g. using "gparted"
Can you explain what you mean by 2nd ext4 partition?
there is a 2nd partition which is ext4 filesystem rather than FAT. It has lots of benefits like ownerships, journaling, ... in contrast to FAT.
Is this partition empty for now?
no, it contains pretty much everything apart from the kernel which has to be on the FAT partition in order for the bootloader to load it
Can i resize the first partition (the one I am currently on - 50MB) to 16 GB?
you may resize to a bigger FAT partition - however, it's not a completely trivial task.
The question is why you would want to do so - as Linux is anyways on the 2nd partition. For the 2nd partition - yes, it can be resized to fill the complete rest of the flash drive (minus 50 MB FAT partition)
I was thinking to change the FAT partition as all the libraries that i need and everything else is installed there. i wanted to save myself the trouble of doing the whole process again. But i think when i copy my image to the new partition (non-FAT), everything (installed libraries) would be transferred to the new partition. Am I right? I am on windows so I will see how to change the partition.